Project description:High-throughput sequencing for life-history sorting and for bridging reference sequences in marine Gerromorpha (Insecta: Heteroptera)
Project description:To test if scRNA-seq contains sufficient phylogenetic information to reconstruct a population history of cancer, immunosuppressed NU/J mice were injected with human cancer cells (MDA-MB-231-LM2). The tumors that develop are derived from the same population and thus share a common ancestor, but evolved independently in each mouse and should form separate clades on reconstructed phylogenetic trees when analysed together. We explore and compare results of phylogenetic analyses based on both expression levels and SNVs called from our scRNA-seq data. Both techniques are shown to be useful for reconstructing phylogenetic relationships between cells, refecting the clonal composition of a tumor. Without an explicit error model, standardized expression values appears to be more powerful and informative than the SNV values at a lower computational cost, due to being a by-product of standard expression analysis. Our results suggest that scRNA-seq can be a competitive alternative or useful addition to conventional scDNA-seq phylogenetic reconstruction. Our results open up a new direction of somatic phylogenetics based on scRNA-seq data. Further research is required to refne and improve these approaches to capture the full picture of somatic evolutionary dynamics in cancer.
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
Project description:Acute myeloid leukemia (AML) is a hematological malignancy, associated with unfavorable patient outcome primarily due to disease relapse. Since specific early leukemic hematopoietic stem and progenitor cells (HSPCs) are suggested to be responsible for AML propagation, the present study used single cell analysis (SCA) to detect and explore rare relapse-initiating HSPC clones, appearing already at diagnosis. To address inherent SCA limitations, we developed a unique high-resolution technique capable to follow single cell-derived subclones of heterogeneous HSPC subpopulations during AML evolution. Each of these subclones was evaluated for chemo-resistance, in-vivo leukemogenic potential, mutational profile, and the subclone cell of origin identified using reconstruction of phylogenetic trees. This study, employing combined functional and genomic analyses, unraveled the patient-specific HSPC subpopulations involved in chemo-resistance and determined, at time of diagnosis, the phenotype of the relapse-initiating clone, allowing early prediction of AML recurrence and suggesting novel precise therapeutic targets for relapse prevention.
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species.
2015-01-08 | GSE54339 | GEO
Project description:Mitogenomic Analysis and Phylogenetic Reconstruction of Four Skipper Species (Lepidoptera: Hesperiidae)